Load and format input data

Input: Metadata bacteria: Database_MRB_isolates & database_raw, Mapping results: Mapping in 4 soils and feedback, Phylogeny: Tree compouted from 16s sequences

Phylogeny

Phylogeny without tree using radialNetwork()

Trees

Abundance of isolates in microbiome

Abundance of isolates from strain collection in microbiome datasets of the field & greenhouse Form quantitative values to quantitative. Abundant strains are defined as abundance > 0.1.

Tree with mapping

The tree is annotated with the quantitative abundance data from mapping greenhouse root microbiome dataset and qualitative information on the abundance in field microbiome datasets in the field (Changins, Zurich, Ithaca) and in the greenhouse (Sheffield). The outermost ring indicates the strains used in growth assays.

Abundance AMPO strains

Location_Background Experiment Family Abundance_mean
Changins_B73 field Sphingomonadaceae 0.6158494
Greenhouse_B73 feedback Sphingomonadaceae 5.4337948
Reckenholz_B73 field Sphingomonadaceae 1.0963679
Aurora_W22 field Sphingomonadaceae 3.2212013
Changins_B73 field Rhizobiaceae 0.4031122
Greenhouse_B73 feedback Rhizobiaceae 1.6348278
Reckenholz_B73 field Rhizobiaceae 0.9226987
Aurora_W22 field Rhizobiaceae 0.7081318
Changins_B73 field Moraxellaceae 0.0000000
Reckenholz_B73 field Moraxellaceae 0.0000000
Aurora_W22 field Moraxellaceae 0.0075401
Changins_B73 field Micrococcaceae 0.2421541
Greenhouse_B73 feedback Micrococcaceae 0.1630430
Reckenholz_B73 field Micrococcaceae 0.3605178
Aurora_W22 field Micrococcaceae 0.2343906
Changins_B73 field Microbacteriaceae 0.4527121
Greenhouse_B73 feedback Microbacteriaceae 1.0564132
Reckenholz_B73 field Microbacteriaceae 1.0495033
Aurora_W22 field Microbacteriaceae 0.5498872
Changins_B73 field Enterobacteriaceae 1.2469469
Greenhouse_B73 feedback Enterobacteriaceae 0.7758565
Reckenholz_B73 field Enterobacteriaceae 11.5794241
Aurora_W22 field Enterobacteriaceae 2.0172681
Location_Background Experiment Abundance_sum
Changins_B73 field 2.960775
Greenhouse_B73 feedback 9.063935
Reckenholz_B73 field 15.008512
Aurora_W22 field 6.738419 
sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.3.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/Zurich
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] Cairo_1.6-0        networkD3_0.4      data.tree_1.0.0    ggnewscale_0.4.9  
##  [5] ggsci_3.0.0        wesanderson_0.3.6  ggtree_3.8.0       ape_5.7-1         
##  [9] reshape2_1.4.4     ggdendro_0.1.23    pheatmap_1.0.12    RColorBrewer_1.1-3
## [13] tibble_3.2.1       pander_0.6.5       ggpmisc_0.5.4-1    ggpp_0.5.4        
## [17] forcats_1.0.0      stringr_1.5.0      readr_2.1.4        tidyr_1.3.0       
## [21] readxl_1.4.2       ggplot2_3.4.3      magrittr_2.0.3     dplyr_1.1.2       
## [25] plyr_1.8.8        
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4       xfun_0.39          bslib_0.5.0        htmlwidgets_1.6.2 
##  [5] lattice_0.21-8     tzdb_0.4.0         yulab.utils_0.0.6  vctrs_0.6.3       
##  [9] tools_4.3.1        generics_0.1.3     parallel_4.3.1     fansi_1.0.4       
## [13] highr_0.10         pkgconfig_2.0.3    Matrix_1.5-4.1     ggplotify_0.1.0   
## [17] lifecycle_1.0.3    farver_2.1.1       compiler_4.3.1     treeio_1.24.1     
## [21] MatrixModels_0.5-1 munsell_0.5.0      SparseM_1.81       ggfun_0.1.0       
## [25] quantreg_5.95      htmltools_0.5.5    sass_0.4.6         lazyeval_0.2.2    
## [29] yaml_2.3.7         pillar_1.9.0       jquerylib_0.1.4    ellipsis_0.3.2    
## [33] MASS_7.3-60        cachem_1.0.8       nlme_3.1-162       tidyselect_1.2.0  
## [37] aplot_0.1.10       digest_0.6.31      stringi_1.7.12     purrr_1.0.1       
## [41] labeling_0.4.2     splines_4.3.1      fastmap_1.1.1      colorspace_2.1-0  
## [45] cli_3.6.1          patchwork_1.1.2    survival_3.5-5     utf8_1.2.3        
## [49] withr_2.5.0        scales_1.2.1       rmarkdown_2.22     igraph_1.5.0      
## [53] cellranger_1.1.0   hms_1.1.3          evaluate_0.21      knitr_1.43        
## [57] gridGraphics_0.5-1 rlang_1.1.1        Rcpp_1.0.11        tidytree_0.4.2    
## [61] glue_1.6.2         polynom_1.4-1      rstudioapi_0.14    jsonlite_1.8.5    
## [65] R6_2.5.1